1 Answer
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Quickly 12.08.1 did not "wipe" commandline arguments from your program. It just moved them from bin/project_name to project_name/__init__.py. There you will find the parse_options function, which you can edit to your liking.

Second question: I can not speak for the quickly developers, but my guess would be that it is easier to upgrade a project, if you move code that has to change in every project away from code which will probably not change.

Third point (although you did not ask...): Quickly is just a tool to help you coding. If you would like to change code inside a DO NOT EDIT THIS FILE block, just go ahead and edit it! Nothing horrible will happen. There is no magic involved, just make sure to check (with bzr diff or similar) what part of your code has changed before you commit your project.